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PCDHGA3 Gene

protein-coding   GIFtS: 40
GCID: GC05P141375

Protocadherin Gamma Subfamily A, 3

  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Protocadherin Gamma Subfamily A, 31 2
PCDH-GAMMA-A32
Protocadherin Gamma-A32
PCDH-gamma-A33

External Ids:    HGNC: 87011   Entrez Gene: 561122   Ensembl: ENSG000002542457   OMIM: 6062905   UniProtKB: Q9Y5H03   

Export aliases for PCDHGA3 gene to outside databases

Previous GC identifers: GC05P140540 GC05P141302 GC05P140702 GC05P140747 GC05P140781 GC05P140699 GC05P140810 GC05P141035 GC05P135868 GC05P141101 GC05P141139 GC05P141179 GC05P141210 GC05P141249 GC05P141297


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PCDHGA3 Gene:
This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on
chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism
may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3
subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more
distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed
by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes
the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region
exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a
critical role in the establishment and function of specific cell-cell connections in the brain. Alternative
splicing has been described for the gamma cluster genes. (provided by RefSeq, Jul 2008)

GeneCards Summary for PCDHGA3 Gene:
PCDHGA3 (protocadherin gamma subfamily A, 3) is a protein-coding gene. Diseases associated with PCDHGA3 include neuronitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB11.

UniProtKB/Swiss-Prot: PCDG3_HUMAN, Q9Y5H0
Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
of specific neuronal connections in the brain




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the PCDHGA3 gene promoter:
         Max1   AREB6   Sp1   AP-1   ATF-2   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHGA3 promoter sequence
   Search Chromatin IP Primers for PCDHGA3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDHGA3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q31   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31

PCDHGA3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHGA3 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P141375:  view genomic region     (about GC identifiers)

Start:
140,723,601 bp from pter      End:
140,892,546 bp from pter
Size:
168,946 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: PCDG3_HUMAN, Q9Y5H0 (See protein sequence)
Recommended Name: Protocadherin gamma-A3 precursor  
Size: 932 amino acids; 100971 Da
Secondary accessions: Q9Y5D4
Alternative splicing: 2 isoforms:  Q9Y5H0-1   Q9Y5H0-2   

Explore the universe of human proteins at neXtProt for PCDHGA3: NX_Q9Y5H0

Explore proteomics data for PCDHGA3 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn265, Asn419, Asn545, Asn685
  • Modification sites at PhosphoSitePlus

  • See PCDHGA3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_061739.2  NP_114400.1  

    ENSEMBL proteins: 
     ENSP00000253812  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    PCDHC: Cadherins / Protocadherins : Clustered

    4 InterPro protein domains:
     IPR015919 Cadherin-like
     IPR013164 Cadherin_N
     IPR020894 Cadherin_CS
     IPR002126 Cadherin

    Graphical View of Domain Structure for InterPro Entry Q9Y5H0

    ProtoNet protein and cluster: Q9Y5H0

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDG3_HUMAN, Q9Y5H0
    Similarity: Contains 6 cadherin domains


    PCDHGA3 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PCDG3_HUMAN, Q9Y5H0
    Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
    of specific neuronal connections in the brain

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    PCDHGA3 for ontologies           About GeneDecksing


    Animal Models:
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    Selected qRT-PCR Assays for microRNAs that regulate PCDHGA3 (see all 29):
    hsa-miR-1226 hsa-miR-448 hsa-miR-4272 hsa-miR-765 hsa-miR-624* hsa-miR-650 hsa-miR-3150a-3p hsa-miR-548a-3p
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PCDG3_HUMAN, Q9Y5H0: Cell membrane; Single-pass type I membrane protein (By similarity)

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    PCDHGA3 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PCDHGA3
    Interactions:

        Search GeneGlobe Interaction Network for PCDHGA3

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007156homophilic cell adhesion IEA--

    PCDHGA3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PCDHGA3 (PCDG3)

    1 HMDB Compound for PCDHGA3    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for PCDHGA3 gene (2 alternative transcripts): 
    NM_018916.3  NM_032011.1  

    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000253812(uc003ljm.2)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate PCDHGA3 (see all 29):
    hsa-miR-1226 hsa-miR-448 hsa-miR-4272 hsa-miR-765 hsa-miR-624* hsa-miR-650 hsa-miR-3150a-3p hsa-miR-548a-3p
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      QuantiTect SYBR Green Assays in human, mouse, rat PCDHGA3
      QuantiFast Probe-based Assays in human, mouse, rat PCDHGA3

    Selected AceView cDNA sequences (see all 737):

    NM_032009 BQ681117 NM_018924 BM702196 NM_032086 NM_031993 BF513666 NM_032087 
    AW089227 BG818666 NM_032403 AW407884 BQ018446 AF152521 BM694643 AF152504 
    BG912888 BF511055 CA388789 CR614457 AF152520 BC019299 AF152322 NM_018912 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PCDHGA3 expression in normal human tissues (normalized intensities)      PCDHGA3 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHGA3 Expression
    About this image


    PCDHGA3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Lung (Respiratory System)
             Alveolar type II cells
    PCDHGA3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PCDHGA3 Protein Expression

    Genevestigator expression for PCDHGA3
        Custom PCR Arrays for PCDHGA3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHGA3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for PCDHGA3 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhga31 , 5 protocadherin gamma subfamily A, 31, 5 83.3(n)1
    85.84(a)1
      18 (19.55 cM)5
    937111  NM_033586.21  NP_291064.11 
     376743355 
    chicken
    (Gallus gallus)
    Aves --
    --
    Uncharacterized protein
    50(a)
    50(a)
    many ↔ many
    many ↔ many
    13(1193472-1213360)
    13(1131593-1134055)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 8)
    Uncharacterized protein
    Protocadherin gamma a1 unspliced isoform; Uncharac...
    (see all 8)
    54(a)
    54(a)
    (see all 8)
    many ↔ many
    many ↔ many
    (see all 8)
    4(76884496-76886922)
    4(76920849-76923332)


    ENSEMBL Gene Tree for PCDHGA3 (if available)
    TreeFam Gene Tree for PCDHGA3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PCDHGA3 gene
    PCDHB112  PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  ENSG000002556222  PCDHB122  
    PCDHB142  PCDHGA102  PCDHB82  PCDHGB42  PCDHGB12  PCDHGA22  PCDHGA122  PCDHGB22  
    PCDHGA92  PCDHGA82  PCDHGB32  PCDHGA112  PCDHB32  PCDHGA62  PCDHGB62  PCDHGA52  
    PCDHB62  PCDHGC52  PCDHGC42  PCDHB52  PCDHB132  PCDHGA12  PCDHB102  PCDHB12  
    PCDHGA42  PCDHGB72  PCDHGA72  PCDHB42  
    Selected SIMAP similar genes for PCDHGA3 using alignment to 5 protein entries:     PCDG3_HUMAN (see all proteins) (see all similar genes):
    PCDHGA2    PCDHGA4    PCDHGA7    PCDHGA8    PCDHGA1    PCDHGA10
    PCDHGA5    PCDHGA11    PCDHGA12    PCDHGA9    PCDHGA6    PCDHGC3
    ME3    PCDHGB2    PCDHGB7    PCDHGB4    PCDHGB5    PCDHGB1

    PCDHGA3 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    3 SNPs for PCDHGA3    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs77365411,2,4
    ----see VAR_0591902 mis40--------
    rs115759481,2,4
    ----see VAR_0555892 mis40--------
    rs115759471,2,4
    ----see VAR_0555882 mis40--------

    HapMap Linkage Disequilibrium report for PCDHGA3 (140723601 - 140892546 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for PCDHGA3 (see all 15):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2730847CNV Deletion23290073
    esv267823CNV Insertion20981092
    nsv823280CNV Loss20364138
    nsv462470CNV Loss19166990
    nsv327707CNV Loss16902084
    dgv6351n71CNV Loss21882294
    nsv882990CNV Loss21882294
    dgv6352n71CNV Loss21882294
    nsv518799CNV Loss19592680
    dgv6353n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing PCDHGA3
    DNA2.0 Custom Variant and Variant Library Synthesis for PCDHGA3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 606290    OMIM disorders: --

    1 disease for PCDHGA3:    About MalaCards
    neuronitis


    PCDHGA3 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PCDHGA3
    Human Genome Epidemiology (HuGE) Navigator: PCDHGA3 (1 document)

    Export disorders for PCDHGA3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PCDHGA3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with PCDHGA3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PubMed id 10380929)1, 2, 3 Wu Q. and Maniatis T. (Cell 1999)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    3. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (Nature 2004)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (Genome Res. 2001)
    6. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (PubMed id 10835267)1 Nollet F....van Roy F. (J. Mol. Biol. 2000)
    7. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (Proc. Natl. Acad. Sci. U.S.A. 2000)
    8. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)1 Yagi T. and Takeichi M. (amp 2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 56112 HGNC: 8701 AceView: PCDHGC3 Ensembl:ENSG00000254245 euGenes: HUgn56112
    ECgene: PCDHGA3 H-InvDB: PCDHGA3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PCDHGA3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PCDHGA3 gene:
    Search GeneIP for patents involving PCDHGA3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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